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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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2
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Scarpin MR, Simmons CH, Brunkard JO. Translating across kingdoms: target of rapamycin promotes protein synthesis through conserved and divergent pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7016-7025. [PMID: 35770874 PMCID: PMC9664230 DOI: 10.1093/jxb/erac267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
mRNA translation is the growth rate-limiting step in genome expression. Target of rapamycin (TOR) evolved a central regulatory role in eukaryotes as a signaling hub that monitors nutrient availability to maintain homeostasis and promote growth, largely by increasing the rate of translation initiation and protein synthesis. The dynamic pathways engaged by TOR to regulate translation remain debated even in well-studied yeast and mammalian models, however, despite decades of intense investigation. Recent studies have firmly established that TOR also regulates mRNA translation in plants through conserved mechanisms, such as the TOR-LARP1-5'TOP signaling axis, and through pathways specific to plants. Here, we review recent advances in our understanding of the regulation of mRNA translation in plants by TOR.
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Affiliation(s)
- M Regina Scarpin
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
- Department of Plant and Microbial Biology, University of California, Berkeley,CA, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA, USA
| | - Carl H Simmons
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
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3
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Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum. Int J Biol Macromol 2022; 224:1101-1117. [DOI: 10.1016/j.ijbiomac.2022.10.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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4
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Kozlov G, Mattijssen S, Jiang J, Nyandwi S, Sprules T, Iben J, Coon S, Gaidamakov S, Noronha AM, Wilds C, Maraia R, Gehring K. Structural basis of 3'-end poly(A) RNA recognition by LARP1. Nucleic Acids Res 2022; 50:9534-9547. [PMID: 35979957 PMCID: PMC9458460 DOI: 10.1093/nar/gkac696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
La-related proteins (LARPs) comprise a family of RNA-binding proteins involved in a wide range of posttranscriptional regulatory activities. LARPs share a unique tandem of two RNA-binding domains, La motif (LaM) and RNA recognition motif (RRM), together referred to as a La-module, but vary in member-specific regions. Prior structural studies of La-modules reveal they are pliable platforms for RNA recognition in diverse contexts. Here, we characterize the La-module of LARP1, which plays an important role in regulating synthesis of ribosomal proteins in response to mTOR signaling and mRNA stabilization. LARP1 has been well characterized functionally but no structural information exists for its La-module. We show that unlike other LARPs, the La-module in LARP1 does not contain an RRM domain. The LaM alone is sufficient for binding poly(A) RNA with submicromolar affinity and specificity. Multiple high-resolution crystal structures of the LARP1 LaM domain in complex with poly(A) show that it is highly specific for the RNA 3'-end, and identify LaM residues Q333, Y336 and F348 as the most critical for binding. Use of a quantitative mRNA stabilization assay and poly(A) tail-sequencing demonstrate functional relevance of LARP1 RNA binding in cells and provide novel insight into its poly(A) 3' protection activity.
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Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jianning Jiang
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Samuel Nyandwi
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Tara Sprules
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada,Quebec/Eastern Canada NMR Centre, McGill University, Montréal, Canada
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Anne M Noronha
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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5
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Ellis RE. Sex Determination in Nematode Germ Cells. Sex Dev 2022:1-18. [PMID: 35172320 PMCID: PMC9378769 DOI: 10.1159/000520872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Animal germ cells differentiate as sperm or as oocytes. These sexual fates are controlled by complex regulatory pathways to ensure that the proper gametes are made at the appropriate times. SUMMARY Nematodes like Caenorhabditis elegans and its close relatives are ideal models for studying how this regulation works, because the XX animals are self-fertile hermaphrodites that produce both sperm and oocytes. In these worms, germ cells use the same signal transduction pathway that functions in somatic cells. This pathway determines the activity of the transcription factor TRA-1, a Gli protein that can repress male genes. However, the pathway is extensively modified in germ cells, largely by the action of translational regulators like the PUF proteins. Many of these modifications play critical roles in allowing the XX hermaphrodites to make sperm in an otherwise female body. Finally, TRA-1 cooperates with chromatin regulators in the germ line to control the activity of fog-1 and fog-3, which are essential for spermatogenesis. FOG-1 and FOG-3 work together to determine germ cell fates by blocking the translation of oogenic transcripts. Key Messages: Although there is great diversity in how germ cell fates are controlled in other animals, many of the key nematode genes are conserved, and the critical role of translational regulators may be universal.
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Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey, USA
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6
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Fuentes P, Pelletier J, Martinez-Herráez C, Diez-Obrero V, Iannizzotto F, Rubio T, Garcia-Cajide M, Menoyo S, Moreno V, Salazar R, Tauler A, Gentilella A. The 40 S-LARP1 complex reprograms the cellular translatome upon mTOR inhibition to preserve the protein synthetic capacity. SCIENCE ADVANCES 2021; 7:eabg9275. [PMID: 34818049 PMCID: PMC8612684 DOI: 10.1126/sciadv.abg9275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Ribosomes execute the transcriptional program in every cell. Critical to sustain nearly all cellular activities, ribosome biogenesis requires the translation of ~200 factors of which 80 are ribosomal proteins (RPs). As ribosome synthesis depends on RP mRNA translation, a priority within the translatome architecture should exist to ensure the preservation of ribosome biogenesis capacity, particularly under adverse growth conditions. Here, we show that under critical metabolic constraints characterized by mTOR inhibition, LARP1 complexed with the 40S subunit protects from ribophagy the mRNAs regulon for ribosome biogenesis and protein synthesis, acutely preparing the translatome to promptly resume ribosomes production after growth conditions return permissive. Characterizing the LARP1-protected translatome revealed a set of 5′TOP transcript isoforms other than RPs involved in energy production and in mitochondrial function, among other processes, indicating that the mTOR-LARP1-5′TOP axis acts at the translational level as a primary guardian of the cellular anabolic capacity.
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Affiliation(s)
- Pedro Fuentes
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Joffrey Pelletier
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Carolina Martinez-Herráez
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Virginia Diez-Obrero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL). L’Hospitalet de Llobregat, Barcelona, Spain
| | - Flavia Iannizzotto
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Teresa Rubio
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Marta Garcia-Cajide
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sandra Menoyo
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Victor Moreno
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL). L’Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Ramón Salazar
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Albert Tauler
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Antonio Gentilella
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
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7
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Dubois C, Gupta S, Mugler A, Félix MA. Temporally regulated cell migration is sensitive to variation in body size. Development 2021; 148:dev196949. [PMID: 33593818 PMCID: PMC10683003 DOI: 10.1242/dev.196949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly, while undergoing three division rounds. We study the final position of two of its great-granddaughters, the end of migration of which was previously shown to depend on a timing mechanism. We find that the variance in their final position is similar to that of other long-range migrating neurons. As expected from the timing mechanism, the position of QR descendants depends on body size, which we varied by changing maternal age or using body size mutants. Using a mathematical model, we show that body size variation is partially compensated for. Applying environmental perturbations, we find that the variance in final position increased following starvation at hatching. The mean position is displaced upon a temperature shift. Finally, highly significant variation was found among C. elegans wild isolates. Overall, this study reveals that the final position of these neurons is quite robust to stochastic variation, shows some sensitivity to body size and to external perturbations, and varies in the species.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Clément Dubois
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
| | - Shivam Gupta
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
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8
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Bayfield MA, Vinayak J, Kerkhofs K, Mansouri-Noori F. La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates. RNA Biol 2021; 18:168-177. [PMID: 30777481 PMCID: PMC7928037 DOI: 10.1080/15476286.2019.1582955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
La shuttles between the nucleus and cytoplasm where it binds nascent RNA polymerase III (pol III) transcripts and mRNAs, respectively. La protects the 3' end of pol III transcribed RNA precursors, such as pre-tRNAs, through the use of a well-characterized UUU-3'OH binding mode. La proteins are also RNA chaperones, and La-dependent RNA chaperone activity is hypothesized to promote pre-tRNA maturation and translation at cellular and viral internal ribosome entry sites via binding sites distinct from those used for UUU-3'OH recognition. Since the publication of La-UUU-3'OH co-crystal structures, biochemical and genetic experiments have expanded our understanding of how La proteins use UUU-3'OH-independent binding modes to make sequence-independent contacts that can increase affinity for ligands and promote RNA remodeling. Other recent work has also expanded our understanding of how La binds mRNAs through contacts to the poly(A) tail. In this review, we focus on advances in the study of La protein-RNA complex surfaces beyond the description of the La-UUU-3'OH binding mode. We highlight recent advances in the functions of expected canonical nucleic acid interaction surfaces, a heightened appreciation of disordered C-terminal regions, and the nature of sequence-independent RNA determinants in La-RNA target binding. We further discuss how these RNA binding modes may have relevance to the function of the La-related proteins.
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Affiliation(s)
- Mark A. Bayfield
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jyotsna Vinayak
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Kyra Kerkhofs
- Department of Biology, York University, Toronto, Ontario, Canada
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9
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Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. Controversies around the function of LARP1. RNA Biol 2021; 18:207-217. [PMID: 32233986 PMCID: PMC7928164 DOI: 10.1080/15476286.2020.1733787] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.
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Affiliation(s)
- Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, USA
| | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université De Montréal, Montreal, Quebec, Canada
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10
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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11
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Al-Ashtal HA, Rubottom CM, Leeper TC, Berman AJ. The LARP1 La-Module recognizes both ends of TOP mRNAs. RNA Biol 2021; 18:248-258. [PMID: 31601159 PMCID: PMC7927982 DOI: 10.1080/15476286.2019.1669404] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/22/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022] Open
Abstract
La-Related Protein 1 (LARP1) is an RNA-binding protein that regulates the stability and translation of mRNAs encoding the translation machinery, including ribosomal proteins and translation factors. These mRNAs are characterized by a 5'-terminal oligopyrimidine (TOP) motif that coordinates their temporal and stoichiometric expression. While LARP1 represses TOP mRNA translation via the C-terminal DM15 region, the role of the N-terminal La-Module in the recognition and translational regulation of TOP mRNAs remains elusive. Herein we show that the LARP1 La-Module also binds TOP motifs, although in a cap-independent manner. We also demonstrate that it recognizes poly(A) RNA. Further, our data reveal that the LARP1 La-Module can simultaneously engage TOP motifs and poly(A) RNA. These results evoke an intriguing molecular mechanism whereby LARP1 could regulate translation and stabilization of TOP transcripts.
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Affiliation(s)
- Hiba A. Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney M. Rubottom
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas C. Leeper
- Department of Chemistry & Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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12
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Scarpin MR, Leiboff S, Brunkard JO. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. eLife 2020; 9:e58795. [PMID: 33054972 PMCID: PMC7584452 DOI: 10.7554/elife.58795] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
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Affiliation(s)
- M Regina Scarpin
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
| | - Samuel Leiboff
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Laboratory of Genetics, University of Wisconsin—MadisonMadisonUnited States
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13
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Radeke LJ, Herman MA. Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia. BMC Microbiol 2020; 20:170. [PMID: 32560629 PMCID: PMC7304212 DOI: 10.1186/s12866-020-01771-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Background Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.
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Affiliation(s)
- Leah J Radeke
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Michael A Herman
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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14
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Wilbertz JH, Voigt F, Horvathova I, Roth G, Zhan Y, Chao JA. Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response. Mol Cell 2019; 73:946-958.e7. [PMID: 30661979 DOI: 10.1016/j.molcel.2018.12.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022]
Abstract
Biological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules (SGs) and processing bodies (PBs) and its effect on translation and degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics, very few mRNAs directly move between SGs and PBs, and that specific RNA-binding proteins can anchor mRNAs within these compartments. During recovery from stress, we show that mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts. Our work provides a framework for using single-molecule measurements to directly investigate the molecular mechanisms of phase-separated compartments within their cellular environment.
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Affiliation(s)
- Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ivana Horvathova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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15
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Porter DF, Prasad A, Carrick BH, Kroll-Connor P, Wickens M, Kimble J. Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. G3 (BETHESDA, MD.) 2019; 9:153-165. [PMID: 30459181 PMCID: PMC6325917 DOI: 10.1534/g3.118.200300] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In Caenorhabditis elegans, FBF (fem-3 Binding Factor) maintains germline stem cells regardless of which gamete is made, but FBF also functions in the process of spermatogenesis. We have begun to "disentangle" these biological roles by asking which FBF targets are gamete-independent, as expected for stem cells, and which are gamete-specific. Specifically, we compared FBF iCLIP binding profiles in adults making sperm to those making oocytes. Normally, XX adults make oocytes. To generate XX adults making sperm, we used a fem-3(gf) mutant requiring growth at 25°; for comparison, wild-type oogenic hermaphrodites were also raised at 25°. Our FBF iCLIP data revealed FBF binding sites in 1522 RNAs from oogenic adults and 1704 RNAs from spermatogenic adults. More than half of these FBF targets were independent of germline gender. We next clustered RNAs by FBF-RNA complex frequencies and found four distinct blocks. Block I RNAs were enriched in spermatogenic germlines, and included validated target fog-3, while Block II and III RNAs were common to both genders, and Block IV RNAs were enriched in oogenic germlines. Block II (510 RNAs) included almost all validated FBF targets and was enriched for cell cycle regulators. Block III (21 RNAs) was enriched for RNA-binding proteins, including previously validated FBF targets gld-1 and htp-1 We suggest that Block I RNAs belong to the FBF network for spermatogenesis, and that Blocks II and III are associated with stem cell functions.
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Affiliation(s)
- Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
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16
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Arias RS, Sobolev VS, Massa AN, Orner VA, Walk TE, Ballard LL, Simpson SA, Puppala N, Scheffler BE, de Blas F, Seijo GJ. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. BMC PLANT BIOLOGY 2018; 18:170. [PMID: 30111278 PMCID: PMC6094572 DOI: 10.1186/s12870-018-1355-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/19/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Aflatoxin contamination in peanut seeds is still a serious problem for the industry and human health. No stable aflatoxin resistant cultivars have yet been produced, and given the narrow genetic background of cultivated peanuts, wild species became an important source of genetic diversity. Wild peanut seeds, however, are not abundant, thus, an effective method of screening for aflatoxin accumulation using minimal seeds is highly desirable. In addition, keeping record of genetic fingerprinting of each accession would be very useful for breeding programs and for the identification of accessions within germplasm collections. RESULTS In this study, we report a method of screening for aflatoxin accumulation that is applicable to the small-size seeds of wild peanuts, increases the reliability by testing seed viability, and records the genetic fingerprinting of the samples. Aflatoxin levels observed among 20 wild peanut species varied from zero to 19000 ng.g-1 and 155 ng.g-1 of aflatoxin B1 and B2, respectively. We report the screening of 373 molecular markers, including 288 novel SSRs, tested on 20 wild peanut species. Multivariate analysis by Neighbor-Joining, Principal Component Analysis and 3D-Principal Coordinate Analysis using 134 (36 %) transferable markers, in general grouped the samples according to their reported genomes. The best 88 markers, those with high fluorescence, good scorability and transferability, are reported with BLAST results. High quality markers (total 98) that discriminated genomes are reported. A high quality marker with UPIC score 16 (16 out of 20 species discriminated) had significant hits on BLAST2GO to a pentatricopeptide-repeat protein, another marker with score 5 had hits on UDP-D-apiose synthase, and a third one with score 12 had BLASTn hits on La-RP 1B protein. Together, these three markers discriminated all 20 species tested. CONCLUSIONS This study provides a reliable method to screen wild species of peanut for aflatoxin resistance using minimal seeds. In addition we report 288 new SSRs for peanut, and a cost-effective combination of markers sufficient to discriminate all 20 species tested. These tools can be used for the systematic search of aflatoxin resistant germplasm keeping record of the genetic fingerprinting of the accessions tested for breeding purpose.
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Affiliation(s)
- Renee S. Arias
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Victor S. Sobolev
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Alicia N. Massa
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Valerie A. Orner
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Travis E. Walk
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Linda L. Ballard
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Sheron A. Simpson
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Naveen Puppala
- New Mexico State University, Agricultural Science Center at Clovis, 2346 SR 288, Clovis, NM 88101 USA
| | - Brian E. Scheffler
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Francisco de Blas
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, C.P, 3400 Corrientes, Argentina
| | - Guillermo J. Seijo
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, C.P, 3400 Corrientes, Argentina
- Instituto de Botánica del Nordeste, (UNNE-CONICET), Casilla de Correo 209, 3400 Corrientes, Argentina
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17
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Fonseca BD, Lahr RM, Damgaard CK, Alain T, Berman AJ. LARP1 on TOP of ribosome production. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1480. [PMID: 29722158 DOI: 10.1002/wrna.1480] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
The ribosome is an essential unit of all living organisms that commands protein synthesis, ultimately fuelling cell growth (accumulation of cell mass) and cell proliferation (increase in cell number). The eukaryotic ribosome consists of 4 ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs). Despite its fundamental role in every living organism, our present understanding of how higher eukaryotes produce the various ribosome components is incomplete. Uncovering the mechanisms utilized by human cells to generate functional ribosomes will likely have far-reaching implications in human disease. Recent biochemical and structural studies revealed La-related protein 1 (LARP1) as a key new player in RP production. LARP1 is an RNA-binding protein that belongs to the LARP superfamily; it controls the translation and stability of the mRNAs that encode RPs and translation factors, which are characterized by a 5' terminal oligopyrimidine (5'TOP) motif and are thus known as TOP mRNAs. The activity of LARP1 is regulated by the mammalian target of rapamycin complex 1 (mTORC1): a eukaryotic protein kinase complex that integrates nutrient sensing with mRNA translation, particularly that of TOP mRNAs. In this review, we provide an overview of the role of LARP1 in the control of ribosome production in multicellular eukaryotes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Bruno D Fonseca
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Roni M Lahr
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | | | - Tommy Alain
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Andrea J Berman
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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18
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Philippe L, Vasseur JJ, Debart F, Thoreen CC. La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region. Nucleic Acids Res 2018; 46:1457-1469. [PMID: 29244122 PMCID: PMC5814973 DOI: 10.1093/nar/gkx1237] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 11/14/2022] Open
Abstract
Cell growth is a complex process shaped by extensive and coordinated changes in gene expression. Among these is the tightly regulated translation of a family of growth-related mRNAs defined by a 5' terminal oligopyrimidine (TOP) motif. TOP mRNA translation is partly controlled via the eukaryotic initiation factor 4F (eIF4F), a translation factor that recognizes the mRNA 5' cap structure. Recent studies have also implicated La-related protein 1 (LARP1), which competes with eIF4F for binding to mRNA 5' ends. However, it has remained controversial whether LARP1 represses TOP mRNA translation directly and, if so, what features define its mRNA targets. Here, we show that the C-terminal half of LARP1 is necessary and sufficient to control TOP mRNA translation in cells. This fragment contains the DM15 cap-binding domain as well as an adjacent regulatory region that we identified. We further demonstrate that purified LARP1 represses TOP mRNA translation in vitro through the combined recognition of both the TOP sequence and cap structure, and that its intrinsic repressive activity and affinity for these features are subject to regulation. These results support a model whereby the translation of TOP mRNAs is controlled by a growth-regulated competition between eIF4F and LARP1 for their 5' ends.
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Affiliation(s)
- Lucas Philippe
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Jean-Jacques Vasseur
- Department of Nucleic Acids, IBMM, Université de Montpellier, CNRS UMR 5247, ENSCM, Montpellier, France
| | - Françoise Debart
- Department of Nucleic Acids, IBMM, Université de Montpellier, CNRS UMR 5247, ENSCM, Montpellier, France
| | - Carson C Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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19
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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20
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Mattijssen S, Arimbasseri AG, Iben JR, Gaidamakov S, Lee J, Hafner M, Maraia RJ. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. eLife 2017; 6:e28889. [PMID: 28895529 PMCID: PMC5626478 DOI: 10.7554/elife.28889] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA function is controlled by the 3' poly(A) tail (PAT) and poly(A)-binding protein (PABP). La-related protein-4 (LARP4) binds poly(A) and PABP. LARP4 mRNA contains a translation-dependent, coding region determinant (CRD) of instability that limits its expression. Although the CRD comprises <10% of LARP4 codons, the mRNA levels vary >20 fold with synonymous CRD substitutions that accommodate tRNA dynamics. Separately, overexpression of the most limiting tRNA increases LARP4 levels and reveals its functional activity, net lengthening of the PATs of heterologous mRNAs with concomitant stabilization, including ribosomal protein (RP) mRNAs. Genetic deletion of cellular LARP4 decreases PAT length and RPmRNA stability. This LARP4 activity requires its PABP-interaction domain and the RNA-binding module which we show is sensitive to poly(A) 3'-termini, consistent with protection from deadenylation. The results indicate that LARP4 is a posttranscriptional regulator of ribosomal protein production in mammalian cells and suggest that this activity can be controlled by tRNA levels.
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Affiliation(s)
- Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | | | - James R Iben
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Joowon Lee
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Markus Hafner
- National Institute of Arthritis and Musculoskeletal and Skin DiseasesNational Institutes of HealthBethesdaUnited States
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
- Commissioned CorpsUS Public Health ServiceBethesdaUnited Staes
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21
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Hopkins TG, Mura M, Al-Ashtal HA, Lahr RM, Abd-Latip N, Sweeney K, Lu H, Weir J, El-Bahrawy M, Steel JH, Ghaem-Maghami S, Aboagye EO, Berman AJ, Blagden SP. The RNA-binding protein LARP1 is a post-transcriptional regulator of survival and tumorigenesis in ovarian cancer. Nucleic Acids Res 2016; 44:1227-46. [PMID: 26717985 PMCID: PMC4756840 DOI: 10.1093/nar/gkv1515] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/12/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are increasingly identified as post-transcriptional drivers of cancer progression. The RBP LARP1 is an mRNA stability regulator, and elevated expression of the protein in hepatocellular and lung cancers is correlated with adverse prognosis. LARP1 associates with an mRNA interactome that is enriched for oncogenic transcripts. Here we explore the role of LARP1 in epithelial ovarian cancer, a disease characterized by the rapid acquisition of resistance to chemotherapy through the induction of pro-survival signalling. We show, using ovarian cell lines and xenografts, that LARP1 is required for cancer cell survival and chemotherapy resistance. LARP1 promotes tumour formation in vivo and maintains cancer stem cell-like populations. Using transcriptomic analysis following LARP1 knockdown, cross-referenced against the LARP1 interactome, we identify BCL2 and BIK as LARP1 mRNA targets. We demonstrate that, through an interaction with the 3' untranslated regions (3' UTRs) of BCL2 and BIK, LARP1 stabilizes BCL2 but destabilizes BIK with the net effect of resisting apoptosis. Together, our data indicate that by differentially regulating the stability of a selection of mRNAs, LARP1 promotes ovarian cancer progression and chemotherapy resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Autoantigens/genetics
- Autoantigens/metabolism
- Blotting, Western
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Cell Line, Tumor
- Cell Survival/drug effects
- Cell Survival/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- HeLa Cells
- Humans
- Interleukin Receptor Common gamma Subunit/deficiency
- Interleukin Receptor Common gamma Subunit/genetics
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Microscopy, Confocal
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Protein Binding
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Survival Analysis
- Transplantation, Heterologous
- SS-B Antigen
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Affiliation(s)
- Thomas G Hopkins
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Manuela Mura
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Hiba A Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Normala Abd-Latip
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Katrina Sweeney
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Haonan Lu
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Justin Weir
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Mona El-Bahrawy
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Jennifer H Steel
- Imperial College Experimental Cancer Medicine Centre, Division of Cancer, Imperial College Academic Health Science Centre, London W12 0NN, UK
| | - Sadaf Ghaem-Maghami
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Eric O Aboagye
- Comprehensive Cancer Imaging Centre, Imperial College, Du Cane Road, London W12 0NN, UK
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sarah P Blagden
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK Department of Oncology, University of Oxford, Old Road, Oxford OX3 7LE, UK
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22
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Xiaoli Z, Yawei W, Lianna L, Haifeng L, Hui Z. Screening of Target Genes and Regulatory Function of miRNAs as Prognostic Indicators for Prostate Cancer. Med Sci Monit 2015; 21:3748-59. [PMID: 26628405 PMCID: PMC4671457 DOI: 10.12659/msm.894670] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs expression profiling of prostate cancer is becoming increasingly used due to its usefulness in diagnosis, staging, prognosis, and response to treatment. The aim of this study was to screen differentially expressed miRNAs in prostate cancer and analyze the functions and signal pathways of their target genes. Material/Methods High-throughput data of miRNAs were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 551 samples (52 normal and 499 prostate cancer cases) and 1046 miRNAs expression values were selected for further analysis. Differentially expressed miRNAs between normal and prostate cancer tissues were identified using SAMR. StarBase and TargetScan software were used to predict the miRNAs’ target group and target genes, respectively. GO functional and KEGG pathway analysis was conducted on up/down-regulated expressed miRNA with DAVID. Finally, survival analysis was performed to evaluate the association of differently expressed miRNAs signature and overall survival of prostate cancer patients. Results A total of 162 miRNAs were differentially expressed between normal and prostate cancer samples, including 128 up-regulated and 38 down-regulated ones; hsa-mir-153-2, hsa-mir-92a-1, and hsa-mir-182 (up-regulated); and hsa-mir-29a, hsa-mir-10a, and hsa-mir-221 (down-regulated) were identified as good biomarkers. In GO and KEGG analysis, target genes of down-regulated miRNAs were significantly enriched in positive ion combination and JAK-STAT pathway annotation, respectively; the ones with up-regulated miRNAs were significantly enriched in the function of plasma membrane and MARK signaling pathway annotation, respectively. Patients were categorized into low- or high-score groups according to their risk scores from each miRNA. The patients in the low-score group had better overall survival compared with those in high-score group. Conclusions The 6 differentially expressed miRNAs and their target genes were used to define important molecular targets that could serve as prognostic and predictive markers in the treatment of prostate cancer. Further research on the function of the target genes in the MAPK signal pathway could provide references for treatment of prostate cancer.
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Affiliation(s)
- Zhang Xiaoli
- Life Science Research Center of Hebei North University, Zhangjiakou, Hebei, China (mainland)
| | - Wei Yawei
- Basic Medical College of Hebei North University, Zhangjiakou, Hebei, China (mainland)
| | - Liu Lianna
- College of Laboratory Medicine of Hebei North University, Zhangjiakou, Hebei, China (mainland)
| | - Li Haifeng
- Life Science Research Center of Hebei North University, Zhangjiakou, Hebei, China (mainland)
| | - Zhang Hui
- Basic Medical College of Hebei North University, Zhangjiakou, Hebei, China (mainland)
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Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules 2015; 5:2701-22. [PMID: 26501340 PMCID: PMC4693254 DOI: 10.3390/biom5042701] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Abstract
The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.
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Affiliation(s)
- Chara Stavraka
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
| | - Sarah Blagden
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
- Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LE, UK.
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24
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Lahr RM, Mack SM, Héroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence. Nucleic Acids Res 2015; 43:8077-88. [PMID: 26206669 PMCID: PMC4652764 DOI: 10.1093/nar/gkv748] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/09/2015] [Accepted: 07/11/2015] [Indexed: 12/20/2022] Open
Abstract
La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.
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Affiliation(s)
- Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Seshat M Mack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Annie Héroux
- Photon Sciences Directorate, Bldg 745 L107 Brookhaven National Laboratory Upton, NY 11973, USA
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Cécile Bousquet-Antonelli
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Jean-Marc Deragon
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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25
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Küspert M, Murakawa Y, Schäffler K, Vanselow JT, Wolf E, Juranek S, Schlosser A, Landthaler M, Fischer U. LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation. RNA (NEW YORK, N.Y.) 2015; 21:1294-305. [PMID: 26001795 PMCID: PMC4478348 DOI: 10.1261/rna.051441.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/02/2015] [Indexed: 05/23/2023]
Abstract
mRNAs are key molecules in gene expression and subject to diverse regulatory events. Regulation is accomplished by distinct sets of trans-acting factors that interact with mRNAs and form defined mRNA-protein complexes (mRNPs). The resulting "mRNP code" determines the fate of any given mRNA and thus controlling gene expression at the post-transcriptional level. The La-related protein 4B (LARP4B) belongs to an evolutionarily conserved family of RNA-binding proteins characterized by the presence of a La-module implicated in direct RNA binding. Biochemical experiments have shown previously direct interactions of LARP4B with factors of the translation machinery. This finding along with the observation of an association with actively translating ribosomes suggested that LARP4B is a factor contributing to the mRNP code. To gain insight into the function of LARP4B in vivo we tested its mRNA association at the transcriptome level and its impact on the proteome. PAR-CLIP analyses allowed us to identify the in vivo RNA targets of LARP4B. We show that LARP4B binds to a distinct set of cellular mRNAs by contacting their 3' UTRs. Biocomputational analysis combined with in vitro binding assays identified the LARP4B-binding motif on mRNA targets. The reduction of cellular LARP4B levels leads to a marked destabilization of its mRNA targets and consequently their reduced translation. Our data identify LARP4B as a component of the mRNP code that influences the expression of its mRNA targets by affecting their stability.
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Affiliation(s)
- Maritta Küspert
- Biozentrum Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | | | - Katrin Schäffler
- Biozentrum Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Jens T Vanselow
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, Universität Würzburg, D-97080 Würzburg, Germany
| | - Elmar Wolf
- Biozentrum Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Stefan Juranek
- Biozentrum Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, Universität Würzburg, D-97080 Würzburg, Germany
| | | | - Utz Fischer
- Biozentrum Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, Universität Würzburg, D-97080 Würzburg, Germany Department of Radiation Medicine and Applied Sciences, University of California at San Diego, San Diego, California 92037, USA
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26
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Abstract
PABPs [poly(A)-binding proteins] bind to the poly(A) tail of eukaryotic mRNAs and are conserved in species ranging from yeast to human. The prototypical cytoplasmic member, PABP1, is a multifunctional RNA-binding protein with roles in global and mRNA-specific translation and stability, consistent with a function as a central regulator of mRNA fate in the cytoplasm. More limited insight into the molecular functions of other family members is available. However, the consequences of disrupting PABP function in whole organisms is less clear, particularly in vertebrates, and even more so in mammals. In the present review, we discuss current and emerging knowledge with respect to the functions of PABP family members in whole animal studies which, although incomplete, already underlines their biological importance and highlights the need for further intensive research in this area.
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27
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Deragon JM, Bousquet-Antonelli C. The role of LARP1 in translation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:399-417. [PMID: 25892282 DOI: 10.1002/wrna.1282] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
The LARP1 proteins form an evolutionarily homogeneous subgroup of the eukaryotic superfamily of La-Motif (LAM) containing factors. Members of the LARP1 family are found in most protists, fungi, plants, and animals. We review here evidence suggesting that LARP1 are key versatile messenger RNA (mRNA)-binding proteins involved in regulating important biological processes such as gametogenesis, embryogenesis, sex determination, and cell division in animals, as well as acclimation to stress in yeasts and plants. LARP1 proteins perform all these essential tasks likely by binding to key mRNAs and regulating their stability and/or translation. In human, the impact of LARP1 over cell division and proliferation is potentially under the control of the TORC1 complex. We review data suggesting that LARP1 is a direct target of this master signaling hub. TOR-dependent LARP1 phosphorylation could specifically enhance the translation of TOP mRNAs providing a way to promote translation, growth, and proliferation. Consequently, LARP1 is found to be significantly upregulated in many malignant cell types. In plants, LARP1 was found to act as a cofactor of the heat-induced mRNA degradation process, an essential acclimation strategy leading to the degradation of more than 4500 mRNAs coding for growth and development housekeeping functions. In Saccharomyces cerevisiae, the LARP1 proteins (Slf1p and Sro9p) are important, among other things, for copper resistance and oxidative stress survival. LARP1 proteins are therefore emerging as critical ancient mRNA-binding factors that evolved common as well as specific targets and regulatory functions in all eukaryotic lineages.
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Affiliation(s)
- Jean-Marc Deragon
- CNRS, LGDP-UMR5096, Perpignan, France.,University of Perpignan, LGDP-UMR5096, Perpignan, France
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28
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Meyuhas O, Kahan T. The race to decipher the top secrets of TOP mRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:801-11. [PMID: 25234618 DOI: 10.1016/j.bbagrm.2014.08.015] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/18/2014] [Accepted: 08/27/2014] [Indexed: 12/20/2022]
Abstract
Cells encountering hostile growth conditions, like those residing in the middle of a newly developing solid tumor, conserve resources and energy by downregulating protein synthesis. One mechanism in this response is the translational repression of multiple mRNAs that encode components of the translational apparatus. This coordinated translational control is carried through a common cis-regulatory element, the 5' Terminal OligoPyrimidine motif (5'TOP), after which these mRNAs are referred to as TOP mRNAs. Subsequent to the initial structural and functional characterization of members of this family, the research of TOP mRNAs has progressed in three major directions: a) delineating the landscape of the family; b) establishing the pathways that transduce stress cues into selective translational repression; and c) attempting to decipher the most proximal trans-acting factor(s) and defining its mode of action--a repressor or activator. The present chapter critically reviews the development in these three avenues of research with a special emphasis on the two "top secrets" of the TOP mRNA family: the scope of its members and the identity of the proximal cellular regulator(s). This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Oded Meyuhas
- Department of Biochemistry and Molecular Biology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| | - Tamar Kahan
- Bioinformatics Unit, The Hebrew University, Hadassah Medical School, Jerusalem 91120, Israel
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29
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Kobet RA, Pan X, Zhang B, Pak SC, Asch AS, Lee MH. Caenorhabditis elegans: A Model System for Anti-Cancer Drug Discovery and Therapeutic Target Identification. Biomol Ther (Seoul) 2014; 22:371-83. [PMID: 25414766 PMCID: PMC4201220 DOI: 10.4062/biomolther.2014.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 01/27/2023] Open
Abstract
The nematode Caenorhabditis elegans (C. elegans) offers a unique opportunity for biological and basic medical researches due to its genetic tractability and well-defined developmental lineage. It also provides an exceptional model for genetic, molecular, and cellular analysis of human disease-related genes. Recently, C. elegans has been used as an ideal model for the identification and functional analysis of drugs (or small-molecules) in vivo. In this review, we describe conserved oncogenic signaling pathways (Wnt, Notch, and Ras) and their potential roles in the development of cancer stem cells. During C. elegans germline development, these signaling pathways regulate multiple cellular processes such as germline stem cell niche specification, germline stem cell maintenance, and germ cell fate specification. Therefore, the aberrant regulations of these signaling pathways can cause either loss of germline stem cells or overproliferation of a specific cell type, resulting in sterility. This sterility phenotype allows us to identify drugs that can modulate the oncogenic signaling pathways directly or indirectly through a high-throughput screening. Current in vivo or in vitro screening methods are largely focused on the specific core signaling components. However, this phenotype-based screening will identify drugs that possibly target upstream or downstream of core signaling pathways as well as exclude toxic effects. Although phenotype-based drug screening is ideal, the identification of drug targets is a major challenge. We here introduce a new technique, called Drug Affinity Responsive Target Stability (DARTS). This innovative method is able to identify the target of the identified drug. Importantly, signaling pathways and their regulators in C. elegans are highly conserved in most vertebrates, including humans. Therefore, C. elegans will provide a great opportunity to identify therapeutic drugs and their targets, as well as to understand mechanisms underlying the formation of cancer.
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Affiliation(s)
- Robert A Kobet
- Department of Medicine, Department of Oncology, Division of Hematology/Oncology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Stephen C Pak
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, Pittsburgh, PA 15224
| | - Adam S Asch
- Department of Medicine, Department of Oncology, Division of Hematology/Oncology, Brody School of Medicine, East Carolina University, Greenville, NC 27834 ; Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599 ; Current address: Department of Medicine, Division of Hematology/Oncology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | - Myon-Hee Lee
- Department of Medicine, Department of Oncology, Division of Hematology/Oncology, Brody School of Medicine, East Carolina University, Greenville, NC 27834 ; Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599
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30
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Ashton-Beaucage D, Udell CM, Gendron P, Sahmi M, Lefrançois M, Baril C, Guenier AS, Duchaine J, Lamarre D, Lemieux S, Therrien M. A functional screen reveals an extensive layer of transcriptional and splicing control underlying RAS/MAPK signaling in Drosophila. PLoS Biol 2014; 12:e1001809. [PMID: 24643257 PMCID: PMC3958334 DOI: 10.1371/journal.pbio.1001809] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/05/2014] [Indexed: 12/11/2022] Open
Abstract
A global RNAi screening approach in Drosophila cells identifies a large group of transcription and splicing factors that modulate RAS/MAPK signaling by altering the expression of MAPK. The small GTPase RAS is among the most prevalent oncogenes. The evolutionarily conserved RAF-MEK-MAPK module that lies downstream of RAS is one of the main conduits through which RAS transmits proliferative signals in normal and cancer cells. Genetic and biochemical studies conducted over the last two decades uncovered a small set of factors regulating RAS/MAPK signaling. Interestingly, most of these were found to control RAF activation, thus suggesting a central regulatory role for this event. Whether additional factors are required at this level or further downstream remains an open question. To obtain a comprehensive view of the elements functionally linked to the RAS/MAPK cascade, we used a quantitative assay in Drosophila S2 cells to conduct a genome-wide RNAi screen for factors impacting RAS-mediated MAPK activation. The screen led to the identification of 101 validated hits, including most of the previously known factors associated to this pathway. Epistasis experiments were then carried out on individual candidates to determine their position relative to core pathway components. While this revealed several new factors acting at different steps along the pathway—including a new protein complex modulating RAF activation—we found that most hits unexpectedly work downstream of MEK and specifically influence MAPK expression. These hits mainly consist of constitutive splicing factors and thereby suggest that splicing plays a specific role in establishing MAPK levels. We further characterized two representative members of this group and surprisingly found that they act by regulating mapk alternative splicing. This study provides an unprecedented assessment of the factors modulating RAS/MAPK signaling in Drosophila. In addition, it suggests that pathway output does not solely rely on classical signaling events, such as those controlling RAF activation, but also on the regulation of MAPK levels. Finally, it indicates that core splicing components can also specifically impact alternative splicing. The RAS/MAPK pathway is a cornerstone of the cell proliferation signaling apparatus. It has a notable involvement in cancer as mutations in the components of the pathway are associated with aberrant proliferation. Previous work has focused predominantly on post-translational regulation of RAS/MAPK signaling such that a large and intricate network of factors is now known to act on core pathway components. However, regulation at the pre-translational level has not been examined nearly as extensively and is comparatively poorly understood. In this study, we used an unbiased and global screening approach to survey the Drosophila genome—using Drosophila cultured cells—for novel regulators of this pathway. Surprisingly, a majority of our hits were associated to either transcription or mRNA splicing. We used a series of secondary screening assays to determine which part of the RAS/MAPK pathway these candidates target. We found that these factors were not equally distributed along the pathway, but rather converged predominantly on mapk mRNA expression and processing. Our findings raise the intriguing possibility that regulation of mapk transcript production is a key step for a diverse set of regulatory inputs, and may play an important part in RAS/MAPK signaling dynamics.
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Affiliation(s)
- Dariel Ashton-Beaucage
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Christian M. Udell
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Martin Lefrançois
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Caroline Baril
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Anne-Sophie Guenier
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Jean Duchaine
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
| | - Daniel Lamarre
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
- Département de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
- Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Québec, Canada
- Département de pathologie et de biologie cellulaire, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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31
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Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP. Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation. Genes Dev 2014; 28:357-71. [PMID: 24532714 PMCID: PMC3937514 DOI: 10.1101/gad.231407.113] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022]
Abstract
The mammalian target of rapamycin (mTOR) promotes cell growth and proliferation by promoting mRNA translation and increasing the protein synthetic capacity of the cell. Although mTOR globally promotes translation by regulating the mRNA 5' cap-binding protein eIF4E (eukaryotic initiation factor 4E), it also preferentially regulates the translation of certain classes of mRNA via unclear mechanisms. To help fill this gap in knowledge, we performed a quantitative proteomic screen to identify proteins that associate with the mRNA 5' cap in an mTOR-dependent manner. Using this approach, we identified many potential regulatory factors, including the putative RNA-binding protein LARP1 (La-related protein 1). Our results indicate that LARP1 associates with actively translating ribosomes via PABP and that LARP1 stimulates the translation of mRNAs containing a 5' terminal oligopyrimidine (TOP) motif, encoding for components of the translational machinery. We found that LARP1 associates with the mTOR complex 1 (mTORC1) and is required for global protein synthesis as well as cell growth and proliferation. Together, these data reveal important molecular mechanisms involved in TOP mRNA translation and implicate LARP1 as an important regulator of cell growth and proliferation.
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Affiliation(s)
- Joseph Tcherkezian
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Marie Cargnello
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Yves Romeo
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, 31062 Toulouse, Cedex 04, France
- Université de Toulouse, Université Paul Sabatier (UPS), F-31000 Toulouse, France
| | - Edward L. Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Genevieve Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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32
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Merret R, Descombin J, Juan YT, Favory JJ, Carpentier MC, Chaparro C, Charng YY, Deragon JM, Bousquet-Antonelli C. XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress. Cell Rep 2013; 5:1279-93. [DOI: 10.1016/j.celrep.2013.11.019] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 10/08/2013] [Accepted: 11/09/2013] [Indexed: 01/22/2023] Open
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Xie C, Huang L, Xie S, Xie D, Zhang G, Wang P, Peng L, Gao Z. LARP1 predict the prognosis for early-stage and AFP-normal hepatocellular carcinoma. J Transl Med 2013; 11:272. [PMID: 24159927 PMCID: PMC3814951 DOI: 10.1186/1479-5876-11-272] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/24/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The La-related protein 1 (LARP1) has been found to be a RNA binding protein and was related to spermatogenesis, embryogenesis and cell-cycle progression. The aim of this study was to investigate the prognostic value of LARP1 in hepatocellular carcinoma (HCC). METHODS LARP1 expression was examined in 15 HCC cell lines and 272 clinical specimens using real-time PCR, immunohistochemistry (IHC) and western blot analysis (WB). LARP1 expression was also studied in 6 paired HCC lesions and the adjacent non-cancerous tissue samples. Statistical analyses were applied to derive association between LARP1 expression scores and clinical characters as well as patient survival. RESULTS mRNA and protein levels of LARP1 were higher in HCC cell lines and HCC lesions than in normal liver epithelial cells and the paired adjacent noncancerous tissues. LARP1 expression was correlated to survival time, vital status, tumor size and Child-Pugh score. Overall survival analysis showed HCC patients with high LARP1 expression level had lower survival rate (P<0.01). Importantly, this correlation remained significant in patients with early-stage HCC or with normal serum AFP level. CONCLUSIONS LARP1 protein may represent a promising biomarker for predicting the prognosis of HCC, including in early-stage and AFP-normal patients.
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Affiliation(s)
- Chan Xie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Li Huang
- Department of nephrology, The Third affiliated hospital of Guangzhou medical university, Guangzhou, China
| | - Shibin Xie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
| | - Dongying Xie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
| | - Genlin Zhang
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
| | - Peipei Wang
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
| | - Liang Peng
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
| | - Zhiliang Gao
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, 600# TianHe Road, Guangzhou 510630, Guangdong Province, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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34
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Eswaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SAW, Polyak K, Florea LD, Kumar R. RNA sequencing of cancer reveals novel splicing alterations. Sci Rep 2013; 3:1689. [PMID: 23604310 PMCID: PMC3631769 DOI: 10.1038/srep01689] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/01/2013] [Indexed: 12/30/2022] Open
Abstract
Breast cancer transcriptome acquires a myriad of regulation changes, and splicing is critical for the cell to “tailor-make” specific functional transcripts. We systematically revealed splicing signatures of the three most common types of breast tumors using RNA sequencing: TNBC, non-TNBC and HER2-positive breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We validated the presence of novel hybrid isoforms of critical molecules like CDK4, LARP1, ADD3, and PHLPP2. Our study provides the first comprehensive portrait of transcriptional and splicing signatures specific to breast cancer sub-types, as well as previously unknown transcripts that prompt the need for complete annotation of tissue and disease specific transcriptome.
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Affiliation(s)
- Jeyanthy Eswaran
- McCormick Genomic and Proteomics Center, The George Washington University, Washington, District of Columbia 20037, USA
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35
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Stefanovic B. RNA protein interactions governing expression of the most abundant protein in human body, type I collagen. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:535-45. [PMID: 23907854 PMCID: PMC3748166 DOI: 10.1002/wrna.1177] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Type I collagen is the most abundant protein in human body. The protein turns over slowly and its replacement synthesis is low. However, in wound healing or in pathological fibrosis the cells can increase production of type I collagen several hundred fold. This increase is predominantly due to posttranscriptional regulation, including increased half-life of collagen messenger RNAs (mRNAs) and their increased translatability. Type I collagen is composed of two α1 and one α2 polypeptides that fold into a triple helix. This stoichiometry is strictly regulated to prevent detrimental synthesis of α1 homotrimers. Collagen polypeptides are co-translationally modified and the rate of modifications is in dynamic equilibrium with the rate of folding, suggesting coordinated translation of collagen α1(I) and α2(I) polypeptides. Collagen α1(I) mRNA has in the 3' untranslated region (UTR) a C-rich sequence that binds protein αCP, this binding stabilizes the mRNA in collagen producing cells. In the 5' UTR both collagen mRNAs have a conserved stem-loop (5' SL) structure. The 5' SL is critical for high collagen expression, knock in mice with disruption of the 5' SL are resistant to liver fibrosis. the 5' SL binds protein LARP6 with strict sequence specificity and high affinity. LARP6 recruits RNA helicase A to facilitate translation initiation and associates collagen mRNAs with vimentin and nonmuscle myosin filaments. Binding to vimentin stabilizes collagen mRNAs, while nonmuscle myosin regulates coordinated translation of α1(I) and α2(I) mRNAs. When nonmuscle myosin filaments are disrupted the cells secrete only α1 homotrimers. Thus, the mechanism governing high collagen expression involves two RNA binding proteins and development of cytoskeletal filaments.
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Affiliation(s)
- Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA.
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36
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Goodier JL, Cheung LE, Kazazian HH. Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res 2013; 41:7401-19. [PMID: 23749060 PMCID: PMC3753637 DOI: 10.1093/nar/gkt512] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 05/07/2013] [Accepted: 05/12/2013] [Indexed: 12/22/2022] Open
Abstract
LINE1s occupy 17% of the human genome and are its only active autonomous mobile DNA. L1s are also responsible for genomic insertion of processed pseudogenes and >1 million non-autonomous retrotransposons (Alus and SVAs). These elements have significant effects on gene organization and expression. Despite the importance of retrotransposons for genome evolution, much about their biology remains unknown, including cellular factors involved in the complex processes of retrotransposition and forming and transporting L1 ribonucleoprotein particles. By co-immunoprecipitation of tagged L1 constructs and mass spectrometry, we identified proteins associated with the L1 ORF1 protein and its ribonucleoprotein. These include RNA transport proteins, gene expression regulators, post-translational modifiers, helicases and splicing factors. Many cellular proteins co-localize with L1 ORF1 protein in cytoplasmic granules. We also assayed the effects of these proteins on cell culture retrotransposition and found strong inhibiting proteins, including some that control HIV and other retroviruses. These data suggest candidate cofactors that interact with the L1 to modulate its activity and increase our understanding of the means by which the cell coexists with these genomic 'parasites'.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine
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37
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Abstract
Receptor Tyrosine Kinase (RTK)-Ras-Extracellular signal-regulated kinase (ERK) signaling pathways control many aspects of C. elegans development and behavior. Studies in C. elegans helped elucidate the basic framework of the RTK-Ras-ERK pathway and continue to provide insights into its complex regulation, its biological roles, how it elicits cell-type appropriate responses, and how it interacts with other signaling pathways to do so. C. elegans studies have also revealed biological contexts in which alternative RTK- or Ras-dependent pathways are used instead of the canonical pathway.
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Affiliation(s)
- Meera V Sundaram
- Dept. of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6145, USA.
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Aoki K, Adachi S, Homoto M, Kusano H, Koike K, Natsume T. LARP1 specifically recognizes the 3' terminus of poly(A) mRNA. FEBS Lett 2013; 587:2173-8. [PMID: 23711370 DOI: 10.1016/j.febslet.2013.05.035] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 01/06/2023]
Abstract
A poly(A) tail functions in mRNA turnover and in facilitating translation as a ribonucleoprotein complex with poly(A) binding proteins (PABPs). However, factors that associate with the poly(A) tail other than PABPs have not been described. Using proteomics, we identified candidate proteins that interact to the 3' terminus of the poly(A) tail. Among these proteins, we focused on La motif-related protein 1 (LARP1) and found that LARP1 specifically recognizes the 3' termini of normal poly(A) tails. We also reveal that LARP1 stabilizes multiple mRNAs carrying 5' terminal oligopyrimidine tract (5'TOP). Our findings suggest that LARP1 may be involved in the post-transcriptional regulation of gene expression, at least in several 5'TOP mRNAs, through the binding to 3' terminus of the poly(A) tail.
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Affiliation(s)
- Kazuma Aoki
- Molecular Profiling Research Center for Drug Discovery(molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koutou, Tokyo 135-0064, Japan
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Zanetti S, Puoti A. Sex Determination in the Caenorhabditis elegans Germline. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:41-69. [DOI: 10.1007/978-1-4614-4015-4_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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Merret R, Martino L, Bousquet-Antonelli C, Fneich S, Descombin J, Billey É, Conte MR, Deragon JM. The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins. RNA (NEW YORK, N.Y.) 2013; 19:36-50. [PMID: 23148093 PMCID: PMC3527725 DOI: 10.1261/rna.035469.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 05/27/2023]
Abstract
La-related proteins (LARPs) are largely uncharacterized factors, well conserved throughout evolution. Recent reports on the function of human LARP4 and LARP6 suggest that these proteins fulfill key functions in mRNA metabolism and/or translation. We report here a detailed evolutionary history of the LARP4 and 6 families in eukaryotes. Genes coding for LARP4 and 6 were duplicated in the common ancestor of the vertebrate lineage, but one LARP6 gene was subsequently lost in the common ancestor of the eutherian lineage. The LARP6 gene was also independently duplicated several times in the vascular plant lineage. We observed that vertebrate LARP4 and plant LARP6 duplication events were correlated with the acquisition of a PABP-interacting motif 2 (PAM2) and with a significant reorganization of their RNA-binding modules. Using isothermal titration calorimetry (ITC) and immunoprecipitation methods, we show that the two plant PAM2-containing LARP6s (LARP6b and c) can, indeed, interact with the major plant poly(A)-binding protein (PAB2), while the third plant LARP6 (LARP6a) is unable to do so. We also analyzed the RNA-binding properties and the subcellular localizations of the two types of plant LARP6 proteins and found that they display nonredundant characteristics. As a whole, our results support a model in which the acquisition by LARP4 and LARP6 of a PAM2 allowed their targeting to mRNA 3' UTRs and led to their neofunctionalization.
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Affiliation(s)
- Rémy Merret
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Cécile Bousquet-Antonelli
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Julie Descombin
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Élodie Billey
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
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41
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Translational control in the Caenorhabditis elegans germ line. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:205-47. [PMID: 22872479 DOI: 10.1007/978-1-4614-4015-4_8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Translational control is a prevalent form of gene expression regulation in the Caenorhabditis elegans germ line. Linking the amount of protein synthesis to mRNA quantity and translational accessibility in the cell cytoplasm provides unique advantages over DNA-based controls for developing germ cells. This mode of gene expression is especially exploited in germ cell fate decisions and during oogenesis, when the developing oocytes stockpile hundreds of different mRNAs required for early embryogenesis. Consequently, a dense web of RNA regulators, consisting of diverse RNA-binding proteins and RNA-modifying enzymes, control the translatability of entire mRNA expression programs. These RNA regulatory networks are tightly coupled to germ cell developmental progression and are themselves under translational control. The underlying molecular mechanisms and RNA codes embedded in the mRNA molecules are beginning to be understood. Hence, the C. elegans germ line offers fertile grounds for discovering post-transcriptional mRNA regulatory mechanisms and emerges as great model for a systems level understanding of translational control during development.
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42
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Zhang B, Jia J, Yang M, Yan C, Han Y. Overexpression of a LAM domain containing RNA-binding protein LARP1c induces precocious leaf senescence in Arabidopsis. Mol Cells 2012; 34:367-74. [PMID: 22965746 PMCID: PMC3887763 DOI: 10.1007/s10059-012-0111-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/11/2012] [Accepted: 07/26/2012] [Indexed: 12/30/2022] Open
Abstract
Leaf senescence is the final stage of leaf life history, and it can be regulated by multiple internal and external cues. La-related proteins (LARPs), which contain a well-conserved La motif (LAM) domain and normally a canonical RNA recognition motif (RRM) or noncanonical RRM-like motif, are widely present in eukaryotes. Six LARP genes (LARP1a-1c and LARP6a-6c) are present in Arabidopsis, but their biological functions have not been studied previously. In this study, we investigated the biological roles of LARP1c from the LARP1 family. Constitutive or inducible overexpression of LARP1c caused premature leaf senescence. Expression levels of several senescence-associated genes and defense-related genes were elevated upon overexpression of LARP1c. The LARP1c null mutant 1c-1 impaired ABA-, SA-, and MeJA-induced leaf senescence in detached leaves. Gene expression profiles of LARP1c showed age-dependent expression in rosette leaves. Taken together, our results suggest LARP1c is involved in regulation of leaf senescence.
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Affiliation(s)
- Bangyue Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193,
China
| | - Jianheng Jia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193,
China
| | - Min Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193,
China
| | - Chunxia Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193,
China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193,
China
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43
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Isabelle M, Gagné JP, Gallouzi IE, Poirier GG. Quantitative proteomics and dynamic imaging reveal that G3BP-mediated stress granule assembly is poly(ADP-ribose)-dependent following exposure to MNNG-induced DNA alkylation. J Cell Sci 2012; 125:4555-66. [PMID: 22767504 DOI: 10.1242/jcs.106963] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Poly(ADP-ribose) (pADPr) is a heterogenic molecule synthesised from NAD by poly(ADP-ribose) polymerases (PARPs). Many cellular functions from genome integrity surveillance, cell cycle progression and DNA repair to apoptosis are affected by pADPr through its network of associated proteins. Using quantitative proteomics, we established a temporal map of pADPr-associated complexes upon genotoxic stress. Results suggested a strong pADPr association to many proteins involved in stress granule formation, notably the ras-GAP SH3-binding protein G3BP, as well as in the later phases of alkylation-stress-induced responses. Further investigation with dynamic imaging clearly demonstrated a pADPr-dependent initiation of stress granule assembly originating from the nucleus. The co-transfection of G3BP with poly(ADP-ribose) glycohydrolase (PARG) indicates that pADPr is involved in modulating the nuclear translocation of G3BP. Moreover, a peptide pADPr blot assay of G3BP revealed that pADPr binds to the glycine-arginine-rich domain of G3BP. Thereafter, we established a comprehensive G3BP interactome in the presence of pADPr. Our findings establish a novel function for pADPr in the formation of G3BP-induced stress granules upon genotoxic stress.
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Affiliation(s)
- Maxim Isabelle
- Centre de recherche du CHUQ, Laval University, Cancer Department, Québec, Canada
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44
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Zanetti S, Grinschgl S, Meola M, Belfiore M, Rey S, Bianchi P, Puoti A. The sperm-oocyte switch in the C. elegans hermaphrodite is controlled through steady-state levels of the fem-3 mRNA. RNA (NEW YORK, N.Y.) 2012; 18:1385-1394. [PMID: 22635404 PMCID: PMC3383969 DOI: 10.1261/rna.031237.111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 05/01/2012] [Indexed: 06/01/2023]
Abstract
Post-transcriptional control regulates many aspects of germline development in the Caenorhabditis elegans hermaphrodite. This nematode switches from spermatogenesis to oogenesis and is, therefore, capable of self-fertilization. This sperm-oocyte switch requires 3' UTR-mediated repression of the fem-3 mRNA. Loss of fem-3 repression results in continuous spermatogenesis in hermaphrodites. Although several factors regulating fem-3 have been identified, little is known about the mechanisms that control fem-3. Here, we investigate the steady-state levels of the fem-3 transcript and the expression pattern of its protein product. We show that FEM-3 is exclusively present in germ cells that are committed to spermatogenesis. We found that in fem-3(gf)/+ heterozygotes, mutant fem-3 gain-of-function transcripts are more abundant than their wild-type counterpart. Furthermore, we show that the penetrance of the fem-3(gf) allele correlates with inefficient FBF binding and extended poly(A) tail size of fem-3 mRNAs. Finally, we show that wild-type and gain-of-function mutated fem-3 mRNAs associate equally well with polyribosomes. We propose that the fem-3 mRNA is regulated through stabilization rather than through translatability.
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Affiliation(s)
- Simone Zanetti
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Sonja Grinschgl
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Marco Meola
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Marco Belfiore
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Samantha Rey
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Pamela Bianchi
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
| | - Alessandro Puoti
- Department of Biology, University of Fribourg, CH-1700 Fribourg FR, Switzerland
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45
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Schenk L, Meinel DM, Strässer K, Gerber AP. La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast. RNA (NEW YORK, N.Y.) 2012; 18:449-61. [PMID: 22271760 PMCID: PMC3285933 DOI: 10.1261/rna.028506.111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 11/25/2011] [Indexed: 05/31/2023]
Abstract
The La-motif (LAM) is an ancient and ubiquitous RNA-binding domain defining a superfamily of proteins, which comprises the genuine La proteins and La-related proteins (LARPs). In contrast to La, which binds and stabilizes pre-tRNAs and other RNA polymerase III transcripts, data on function and RNA targets of the LARPs have remained scarce. We have undertaken a global approach to elucidate the previously suggested role of the yeast LARP Slf1p in copper homeostasis. By applying RNA-binding protein immunopurification-microarray (RIP-Chip) analysis, we show that Slf1p and its paralog Sro9p copurify with overlapping sets of hundreds of functionally related mRNAs, including many transcripts coding for ribosomal proteins and histones. Interestingly, among these potential RNA targets were also mRNAs coding for proteins critical for protection of cells against elevated copper concentrations. Mutations introduced in the conserved aromatic patch of the LAM in Slf1p drastically impaired both association with its targets and Slf1-mediated protection of cells against toxic copper concentrations. Furthermore, we show that Slf1p stabilizes copper-related mRNA targets in a LAM-dependent manner. These results provide the first evidence for post-transcriptional regulation of factors/pathways implicated in copper homeostasis by a cytoplasmic RBP.
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Affiliation(s)
- Luca Schenk
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dominik M. Meinel
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich (CIPSM), University of Munich, 81377 Munich, Germany
| | - Katja Strässer
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich (CIPSM), University of Munich, 81377 Munich, Germany
| | - André P. Gerber
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
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46
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Whelan JT, Hollis SE, Cha DS, Asch AS, Lee MH. Post-transcriptional regulation of the Ras-ERK/MAPK signaling pathway. J Cell Physiol 2011; 227:1235-41. [DOI: 10.1002/jcp.22899] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Zheng D, Chen CYA, Shyu AB. Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation. RNA (NEW YORK, N.Y.) 2011; 17:1619-34. [PMID: 21750099 PMCID: PMC3162328 DOI: 10.1261/rna.2789611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cellular factors involved in mRNA degradation and translation repression can aggregate into cytoplasmic domains known as GW bodies or mRNA processing bodies (P-bodies). However, current understanding of P-bodies, especially the regulatory aspect, remains relatively fragmentary. To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance, and disassembly, we compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are not recognized as P-body components. The observation suggests that these other cellular proteins may play important roles in regulating P-body dynamics and functions. We further used siRNA-mediated gene knockdown and immunofluorescence microscopy to demonstrate the validity of our in silico analyses. Our combined approach identifies new P-body components and suggests that protein ubiquitination and protein phosphorylation involving 14-3-3 proteins may play critical roles for post-translational modifications of P-body components in regulating P-body dynamics. Our analyses provide not only a global view of human P-body components and their physical interactions but also a wealth of hypotheses to help guide future research on the regulation and function of human P-bodies.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Chyi-Ying A. Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
- Corresponding author.E-mail .
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48
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Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR, Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011; 332:1317-22. [PMID: 21659604 DOI: 10.1126/science.1199498] [Citation(s) in RCA: 824] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mammalian target of rapamycin (mTOR) protein kinase is a master growth promoter that nucleates two complexes, mTORC1 and mTORC2. Despite the diverse processes controlled by mTOR, few substrates are known. We defined the mTOR-regulated phosphoproteome by quantitative mass spectrometry and characterized the primary sequence motif specificity of mTOR using positional scanning peptide libraries. We found that the phosphorylation response to insulin is largely mTOR dependent and that mTOR exhibits a unique preference for proline, hydrophobic, and aromatic residues at the +1 position. The adaptor protein Grb10 was identified as an mTORC1 substrate that mediates the inhibition of phosphoinositide 3-kinase typical of cells lacking tuberous sclerosis complex 2 (TSC2), a tumor suppressor and negative regulator of mTORC1. Our work clarifies how mTORC1 inhibits growth factor signaling and opens new areas of investigation in mTOR biology.
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Affiliation(s)
- Peggy P Hsu
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
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49
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Singh N, Morlock H, Hanes SD. The Bin3 RNA methyltransferase is required for repression of caudal translation in the Drosophila embryo. Dev Biol 2011; 352:104-15. [DOI: 10.1016/j.ydbio.2011.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 01/06/2011] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
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50
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Yang R, Gaidamakov SA, Xie J, Lee J, Martino L, Kozlov G, Crawford AK, Russo AN, Conte MR, Gehring K, Maraia RJ. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol 2011; 31:542-56. [PMID: 21098120 PMCID: PMC3028612 DOI: 10.1128/mcb.01162-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022] Open
Abstract
The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.
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Affiliation(s)
- Ruiqing Yang
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Sergei A. Gaidamakov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Jingwei Xie
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Joowon Lee
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Luigi Martino
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Guennadi Kozlov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amanda K. Crawford
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amy N. Russo
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Maria R. Conte
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Kalle Gehring
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Richard J. Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
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